You can only sync one Org to one Marketo.
You can link to more Marketos using API. There are a few threads on this topic if you search.
In theory, this could be feasible, since you could have multiple sync users. But the complexity and risks are huge. Starting with how you are going to prevent data from flowing back and forth between Marketo instances through SFDC. But if you can establish a clear rule that partitions you SFDC data, that might work. Use sync filters to make this happen, and remember to filter not only leads and contacts, but also accounts and opportunities, campaigns, etc...
The other way would be to use an ETL instead, so that it would contain the rules that could orient data to the proper Marketo instance.
MSI, on it's end, will have to connect to only one of the Marketo instances.